Flagship Pioneering is known for creating startups that aim to answer broad scientific questions in medicine, sustainability and agriculture, a strategy it describes as “leaps.”
On Wednesday, Flagship announced it’s collected another $3.6 billion to develop a fresh batch of platforms and drugs. In an interview with Endpoints News on Wednesday morning, CEO Noubar Afeyan said pharma partnerships are becoming a bigger deal for its companies, as are large language models and machine learning.
Endpoints spoke with the Flagship founder about the firm’s eighth fund, whether its incubation model can be viewed from an efficiency lens, and how the scope of AI is growing. Afeyan says biotech is having its “most visible moment on the planet,” citing vaccines, obesity drugs and other advancements in cancer and immunology.
Below are key takeaways from the interview, edited for clarity:
Partnerships are a ‘bigger and bigger deal’
Collaborating with pharmaceutical companies is becoming a “bigger and bigger deal,” Afeyan said, both for Flagship’s in-house drug development work at Pioneering Medicines and for its individual spinouts.
“Those kinds of partnerships we are learning how to do more effectively,” he said, “and I would say that that is a business model that may well expand over the next two, three years, and we’re hoping that we will become a reliable long-term supplier of innovative assets to the entire pharmaceutical industry.”
Large drugmakers are running into “dramatic patent cliffs,” with hundreds of billions of dollars in revenue to fill, according to Afeyan.
“That’s got to come from someplace,” he said.
The firm and some of its companies have recently forged partnerships with Novo Nordisk and Pfizer in obesity, which could become the biggest market in pharma history.
“The field is dividing up into almost two buckets: people who make bets on very late-stage assets, either as the basis of a startup, knowing that if something hits, then the pharma companies may buy them or the public market would be interested in them,” he said. “Then [there’s the] people who have the resources and the patience to be able to develop entirely new capabilities and see them through, which involves a lot of financing and a lot of partnering.”
Flagship’s sprawling apparatus works for more than just new medicines, Afeyan said. Other areas of its portfolio can often get overlooked.
“Even if you look beyond our therapeutics area, we also participate broadly in the sustainability space and agriculture [and] climate,” he said. “There again are some pretty dramatic food security problems and climate-driven problems.”
The next wave of companies
About half of the companies that Flagship plans to launch with this fund are likely already in the works, with Afeyan noting that the firm typically works on building them for about three years before discussing them publicly.
A big focus is on programmable medicines, or treatments where “you can change something and know exactly the result you’re going to get,” Afeyan said. “That’s easy to do with nucleic acids, whether it’s RNA or DNA, getting nucleic acid medicines delivered to specific cell types, which has been a longstanding problem.”
Within Flagship’s labs, researchers are also working on what Afeyan said they think could be the “next-next versions” of some of the industry’s most sought-after fields: antibody-drug conjugates and radiopharmaceuticals.
What can’t AI do?
Everyone talks about AI, and everyone has opinions about the role of machine learning and large language models in drug discovery and development.
“For every technology that’s promised in our space, there’s 10 times more people who will say it will never work until it does, and then they’ll say, ‘I told you it’ll work,’” Afeyan said.
“We’re in that mode in AI,” he continued. “We’re in the mode of where the limited partners have to ask themselves, ‘Is there any version of where AI doesn’t have a dramatic impact?’ The general answer to that, that they’re hearing from their experts, is no.”
Multiple Flagship companies are doing work in AI, most notably with Generate:Biomedicines, which has raised more than $700 million to create new proteins using artificial intelligence. It has a broad pipeline across immunology, infectious disease and oncology.
Efficiency and uncertainty: Can they go hand in hand?
Afeyan has said Flagship looks to go after uncertain fields in medicine, versus the traditional pharma approach of avoiding “uncertainty at all costs.”
Flagship has created more than 100 companies with this approach in mind over the past 25 years. It wants to create another 25 companies with the latest fund, begging the question of whether it’s become more efficient with how it builds and grows companies over the years.
“Imagine being efficient in resolving uncertainty. It’s kind of hard to do that, since you don’t really know how hard it’s going to be to resolve the uncertainty,” Afeyan said. “But you can certainly get more experience, more confident, more effective at deploying resources at the right questions.”
He’s bullish that new technologies like AI will adjust how Flagship operates.
“Because you use the word ‘efficiency,’ I think we’ve gotten better at it. But boy, is it still not an efficient process, and I worry it will never be,” Afeyan said. “Technologies that are being made available through large language models and generative AI have a pretty distinct role to play there as well.”
AI will “make a gigantic contribution to how we do what we do within Flagship,” he added, not just for the firm itself but also its companies.